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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411
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        Tool Citations

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        About MultiQC

        This report was generated using MultiQC, version 1.29

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2025-08-10, 11:37 IDT based on data in: /lustre1/home/mass/amalia/montipora_mapping/Ariana_samples/logs/hisat2

        General Statistics

        Showing 48/48 rows.
        Sample Name% Aligned
        SRR14864064_hisat2
        62.3%
        SRR14864065_hisat2
        63.9%
        SRR14864066_hisat2
        47.0%
        SRR14864067_hisat2
        71.5%
        SRR14864068_hisat2
        70.5%
        SRR14864069_hisat2
        78.3%
        SRR14864070_hisat2
        80.5%
        SRR14864071_hisat2
        79.4%
        SRR14864072_hisat2
        71.7%
        SRR22293445_hisat2
        56.7%
        SRR22293446_hisat2
        54.3%
        SRR22293447_hisat2
        58.0%
        SRR22293448_hisat2
        61.8%
        SRR22293449_hisat2
        57.6%
        SRR22293450_hisat2
        58.5%
        SRR22293451_hisat2
        54.5%
        SRR22293452_hisat2
        50.7%
        SRR22293453_hisat2
        48.0%
        SRR22293454_hisat2
        49.4%
        SRR22293455_hisat2
        47.2%
        SRR22293456_hisat2
        50.1%
        SRR22293457_hisat2
        46.9%
        SRR22293458_hisat2
        60.0%
        SRR22293459_hisat2
        56.2%
        SRR22293460_hisat2
        52.9%
        SRR22293461_hisat2
        59.3%
        SRR22293462_hisat2
        63.5%
        SRR22293463_hisat2
        59.5%
        SRR22293464_hisat2
        55.9%
        SRR22293465_hisat2
        55.4%
        SRR22293466_hisat2
        56.4%
        SRR22293467_hisat2
        50.4%
        SRR22293468_hisat2
        57.6%
        SRR22293469_hisat2
        62.4%
        SRR22293470_hisat2
        59.6%
        SRR22293471_hisat2
        54.4%
        SRR22293472_hisat2
        61.0%
        SRR22293473_hisat2
        46.8%
        SRR22293474_hisat2
        55.8%
        SRR22293475_hisat2
        55.0%
        SRR22293476_hisat2
        54.1%
        SRR22293477_hisat2
        57.4%
        SRR22293478_hisat2
        56.7%
        SRR22293479_hisat2
        57.8%
        SRR22293480_hisat2
        56.8%
        SRR22293481_hisat2
        59.0%
        SRR22293482_hisat2
        50.9%
        SRR22293483_hisat2
        49.6%

        Bowtie 2 / HiSAT2

        Results from both Bowtie 2 and HISAT2, tools for aligning reads against a reference genome.URL: http://bowtie-bio.sourceforge.net/bowtie2; https://ccb.jhu.edu/software/hisat2DOI: 10.1038/nmeth.1923; 10.1038/nmeth.3317; 10.1038/s41587-019-0201-4

        Single-end alignments

        This plot shows the number of reads aligning to the reference in different ways.

        There are 3 possible types of alignment:

        • SE mapped uniquely: Read has only one occurence in the reference genome.
        • SE multimapped: Read has multiple occurence.
        • SE not aligned: Read has no occurence.
        Created with MultiQC

        Paired-end alignments

        This plot shows the number of reads aligning to the reference in different ways.

        Please note that single mate alignment counts are halved to tally with pair counts properly.

        There are 6 possible types of alignment:

        • PE mapped uniquely: Pair has only one occurence in the reference genome.
        • PE mapped discordantly uniquely: Pair has only one occurence but not in proper pair.
        • PE one mate mapped uniquely: One read of a pair has one occurence.
        • PE multimapped: Pair has multiple occurence.
        • PE one mate multimapped: One read of a pair has multiple occurence.
        • PE neither mate aligned: Pair has no occurence.
        Created with MultiQC